Variant report

Variant	rs13250041
Chromosome Location	chr8:52734305-52734306
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 132 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10086351	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10095651	0.82[AFR][1000 genomes]
rs10095739	0.80[AMR][1000 genomes]
rs10096943	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10110304	0.81[ASN][1000 genomes]
rs10112086	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1022315	0.80[AMR][1000 genomes]
rs1022316	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10435632	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10504128	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1073371	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1073372	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10958298	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10958299	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10958302	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10958303	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11775601	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11777316	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11777386	0.86[AFR][1000 genomes]
rs11777885	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11782696	0.82[AFR][1000 genomes]
rs11782730	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11784921	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11786126	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12334986	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12546934	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12675156	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12675404	0.80[AMR][1000 genomes]
rs12676361	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12680771	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12680958	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12681673	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12682564	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13250860	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13250922	0.88[AFR][1000 genomes]
rs13252580	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13254066	0.88[AFR][1000 genomes]
rs13256408	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13257067	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13257291	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13257720	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13258269	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13261243	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13264242	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13265029	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13266326	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13267846	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13268907	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13268938	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13269881	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13271572	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13272178	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13272467	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13274160	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13275045	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13275235	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13280391	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13280413	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1517304	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1517305	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs16916810	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1914370	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2395857	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3763547	0.81[AFR][1000 genomes]
rs3824266	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4259408	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4291261	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4294173	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4313145	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4324911	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4330683	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4352840	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4361755	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4395889	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4401852	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4442135	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4487755	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4570148	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4584139	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4587320	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4596648	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4612332	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4618684	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4634632	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4642637	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4873206	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4873207	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4873604	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4873606	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4873608	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4873610	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4873613	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4873616	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs5002416	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs5003717	0.90[AFR][1000 genomes]
rs6983163	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6986984	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6990552	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6999031	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6999321	0.90[AFR][1000 genomes]
rs7008057	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7013587	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7014075	0.80[AMR][1000 genomes]
rs7017450	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7460311	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7463120	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7464192	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7465225	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs753540	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs756484	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7818832	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7829408	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7833777	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs882492	0.82[AFR][1000 genomes]
rs884580	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs925761	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs925763	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9298463	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9298464	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9298465	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9298466	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9643466	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9643790	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9643791	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9643792	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9643793	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv967589	chr8:52731031-52735145	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13250041	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52717600-52735200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:52717600-52741800	Weak transcription	Aorta	Aorta
3	chr8:52717800-52734600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr8:52718000-52734800	Weak transcription	Dnd41	blood
5	chr8:52719400-52741800	Weak transcription	Esophagus	oesophagus
6	chr8:52719800-52734600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr8:52720000-52735000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr8:52720800-52735000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr8:52720800-52737000	Weak transcription	Brain Anterior Caudate	brain
10	chr8:52721000-52741000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr8:52722000-52771400	Weak transcription	Gastric	stomach
12	chr8:52722200-52734800	Weak transcription	Lung	lung
13	chr8:52722200-52752000	Weak transcription	Pancreas	Pancrea
14	chr8:52722400-52735000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr8:52722400-52741800	Weak transcription	Right Ventricle	heart
16	chr8:52722600-52734600	Weak transcription	Fetal Kidney	kidney
17	chr8:52722600-52735000	Weak transcription	HSMM	muscle
18	chr8:52722800-52735200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr8:52722800-52735200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr8:52722800-52741000	Weak transcription	Colon Smooth Muscle	Colon
21	chr8:52722800-52741800	Weak transcription	HSMMtube	muscle
22	chr8:52723000-52741600	Weak transcription	Fetal Heart	heart
23	chr8:52726000-52735000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr8:52726000-52741800	Weak transcription	Brain Substantia Nigra	brain
25	chr8:52726800-52734600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr8:52727600-52756800	Weak transcription	Brain Angular Gyrus	brain
27	chr8:52728000-52734400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:52728200-52759200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr8:52728400-52734400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr8:52729800-52735000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr8:52729800-52741600	Weak transcription	Brain Hippocampus Middle	brain
32	chr8:52730000-52734600	Weak transcription	Adipose Nuclei	Adipose
33	chr8:52730400-52734800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr8:52731200-52734800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr8:52731200-52735200	Weak transcription	Spleen	Spleen
36	chr8:52731200-52763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr8:52731200-52771000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr8:52731400-52753400	Weak transcription	NHDF-Ad	bronchial
39	chr8:52731800-52741800	Weak transcription	Psoas Muscle	Psoas
40	chr8:52731800-52745600	Weak transcription	NHEK	skin
41	chr8:52732200-52734800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:52732200-52735600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr8:52732200-52743600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr8:52732200-52746000	Weak transcription	Fetal Brain Male	brain
45	chr8:52732200-52746400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr8:52732800-52735800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr8:52732800-52753600	Weak transcription	Osteobl	bone
48	chr8:52733000-52735600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr8:52733000-52736000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr8:52733000-52736000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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